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A Commentary on Diversity Measures UniFrac in Very Small Sample Size

In phylogenetic, the diversity measures as UniFrac, weighted UniFrac, and normalized weighted UniFrac are used to estimate the closeness between two samples of genetic material sequences. These measures are widely used in microbiology to compare microbial communities. Furthermore, when the sample si...

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Autores principales: Roldán Ahumada, Judith Agueda, Avendaño Garrido, Martha Lorena
Formato: Online Artículo Texto
Lenguaje:English
Publicado: SAGE Publications 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6482663/
https://www.ncbi.nlm.nih.gov/pubmed/31040637
http://dx.doi.org/10.1177/1176934319843515
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author Roldán Ahumada, Judith Agueda
Avendaño Garrido, Martha Lorena
author_facet Roldán Ahumada, Judith Agueda
Avendaño Garrido, Martha Lorena
author_sort Roldán Ahumada, Judith Agueda
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description In phylogenetic, the diversity measures as UniFrac, weighted UniFrac, and normalized weighted UniFrac are used to estimate the closeness between two samples of genetic material sequences. These measures are widely used in microbiology to compare microbial communities. Furthermore, when the sample size is large enough, very good results have been obtained experimentally. However, some authors do not suggest using them when the sample size is very small. Recently, it has been mentioned that the weighted UniFrac measure can be seen as the Kantorovich-Rubinstein metric between the corresponding empirical distributions of samples of genetic material. Also, it is well known that the Kantorovich-Rubinstein metric complies the metric definition. However, one of the main reasons to establish it is that the sample size is large enough. The goal of this article is to prove that the diversity measures UniFrac are not metrics when the sample size is very small, which justifies why it must not be used in that case, but yes the Kantorovich-Rubinstein metric.
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spelling pubmed-64826632019-04-30 A Commentary on Diversity Measures UniFrac in Very Small Sample Size Roldán Ahumada, Judith Agueda Avendaño Garrido, Martha Lorena Evol Bioinform Online Commentary In phylogenetic, the diversity measures as UniFrac, weighted UniFrac, and normalized weighted UniFrac are used to estimate the closeness between two samples of genetic material sequences. These measures are widely used in microbiology to compare microbial communities. Furthermore, when the sample size is large enough, very good results have been obtained experimentally. However, some authors do not suggest using them when the sample size is very small. Recently, it has been mentioned that the weighted UniFrac measure can be seen as the Kantorovich-Rubinstein metric between the corresponding empirical distributions of samples of genetic material. Also, it is well known that the Kantorovich-Rubinstein metric complies the metric definition. However, one of the main reasons to establish it is that the sample size is large enough. The goal of this article is to prove that the diversity measures UniFrac are not metrics when the sample size is very small, which justifies why it must not be used in that case, but yes the Kantorovich-Rubinstein metric. SAGE Publications 2019-04-23 /pmc/articles/PMC6482663/ /pubmed/31040637 http://dx.doi.org/10.1177/1176934319843515 Text en © The Author(s) 2019 http://www.creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (http://www.creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage).
spellingShingle Commentary
Roldán Ahumada, Judith Agueda
Avendaño Garrido, Martha Lorena
A Commentary on Diversity Measures UniFrac in Very Small Sample Size
title A Commentary on Diversity Measures UniFrac in Very Small Sample Size
title_full A Commentary on Diversity Measures UniFrac in Very Small Sample Size
title_fullStr A Commentary on Diversity Measures UniFrac in Very Small Sample Size
title_full_unstemmed A Commentary on Diversity Measures UniFrac in Very Small Sample Size
title_short A Commentary on Diversity Measures UniFrac in Very Small Sample Size
title_sort commentary on diversity measures unifrac in very small sample size
topic Commentary
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6482663/
https://www.ncbi.nlm.nih.gov/pubmed/31040637
http://dx.doi.org/10.1177/1176934319843515
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